1. ComplexHeatmap
  2. Commit 3bb5581b47355dfd9649bc472272b61d2498deb0
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 4cbce102eabb1633fc8980b1374795bfb44507df

Merge branch 'master' of https://github.com/jokergoo/ComplexHeatmap


Commit id: a15bbec76c85c15bc27273ce15f5118ea087132f

refreshed documentatinos


Commit id: b1fe0a94aa09a4a47e5a02383ce662580f057bdc

ColorMapping object has default value for name slot



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 16/07/2015 15:21:23
Showing 62 changed files
NEWS
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@@ -1,5 +1,6 @@
1 1 
 CHANGES in VERSION 1.2.4
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+* name for ColorMapping object has default value now.
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 * legend for continuous values can be set as continuous legends
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 * row title and column title as well as legend title support expression
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 * add `heatmap_legend_title` in `Heatmap` and `ColorMapping`
R/ColorMapping-class.R
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@@ -67,8 +67,9 @@ ColorMapping = function(name, colors = NULL, levels = NULL,
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 	.Object = new("ColorMapping")
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-	if(is.null(name)) {
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-		stop("You should provide name.")
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+	if(missing(name)) {
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+		increase_color_mapping_index()
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+		name = get_color_mapping_index()
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 	}
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 	if(!is.null(colors)) {
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 		if(is.null(levels)) {
R/utils.R
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@@ -5,6 +5,7 @@ INDEX_ENV = new.env()
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 INDEX_ENV$I_HEATMAP = 0
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 INDEX_ENV$I_ANNOTATION = 0
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 INDEX_ENV$I_ROW_ANNOTATION = 0
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+INDEX_ENV$I_COLOR_MAPPING = 0
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 get_heatmap_index = function() {
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 	INDEX_ENV$I_HEATMAP
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@@ -30,6 +31,13 @@ increase_row_annotation_index = function() {
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 	INDEX_ENV$I_ROW_ANNOTATION = INDEX_ENV$I_ROW_ANNOTATION + 1
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 }
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+get_color_mapping_index = function() {
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+    INDEX_ENV$I_COLOR_MAPPING
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+}
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+
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+increase_color_mapping_index = function() {
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+    INDEX_ENV$I_COLOR_MAPPING = INDEX_ENV$I_COLOR_MAPPING + 1
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+}
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 # default colors for matrix or annotations
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 # this function should be improved later
man/AdditiveUnit-class.rd
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@@ -15,5 +15,6 @@ It is only designed for \code{+} generic method so that above three classes can
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 }
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 \examples{
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+
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 # no example
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 NULL}
man/AdditiveUnit.rd
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@@ -27,5 +27,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example
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 NULL}
man/ColorMapping-class.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `ColorMapping` method page
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 NULL}
man/ColorMapping.rd
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@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
man/Heatmap-class.rd
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@@ -72,5 +72,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `Heatmap` method page
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 NULL}
man/Heatmap.rd
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@@ -115,6 +115,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/HeatmapAnnotation-class.rd
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@@ -29,5 +29,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `HeatmapAnnotation` method page
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 NULL}
man/HeatmapAnnotation.rd
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@@ -48,6 +48,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = HeatmapAnnotation(df = df)
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man/HeatmapList-class.rd
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@@ -68,6 +68,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/HeatmapList.rd
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@@ -27,7 +27,9 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \section{Detailes}{
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+
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 There is no public constructor method for the \code{\link{HeatmapList-class}}.}
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 \examples{
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+
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 # no example
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 NULL}
man/SingleAnnotation-class.rd
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@@ -39,5 +39,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # for examples, please go to `SingleAnnotation` method page
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 NULL}
man/SingleAnnotation.rd
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@@ -49,6 +49,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # discrete character
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 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"),
man/add.AdditiveUnit.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-Heatmap-method.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-HeatmapAnnotation-method.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/add_heatmap-HeatmapList-method.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/anno_barplot.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 f = anno_barplot(rnorm(10))
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 grid.newpage(); f(1:10)
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man/anno_boxplot.rd
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@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_boxplot(mat)
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 grid.newpage(); f(1:8)
man/anno_density.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_density(mat)
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 grid.newpage(); f(1:8)
man/anno_histogram.rd
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@@ -26,6 +26,7 @@ Zuguang Gu <z.gu@dkfz.de>
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27 27 
 }
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 \examples{
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+
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 mat = matrix(rnorm(32), nrow = 4)
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 f = anno_histogram(mat)
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 grid.newpage(); f(1:8)
man/anno_points.rd
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@@ -33,5 +33,6 @@ Zuguang Gu <z.gu@dkfz.de>
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34 34 
 }
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 \examples{
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+
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 f = anno_points(rnorm(10))
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 grid.newpage(); f(1:10)}
man/anno_text.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
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30 30 
 }
31 31 
 \examples{
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+
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 mat = matrix(rnorm(100), 10)
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 colnames(mat) = letters[1:10]
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 rownames(mat) = LETTERS[1:10]
man/annotation_legend_size-HeatmapList-method.rd
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@@ -33,5 +33,6 @@ Zuguang Gu <z.gu@dkfz.de>
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34 34 
 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/color_mapping_legend-ColorMapping-method.rd
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@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>
38 38
39 39 
 }
40 40 
 \examples{
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+
41 42 
 # discrete color mapping for characters
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 cm = ColorMapping(name = "test",
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     colors = c("blue", "white", "red"),
man/columnAnnotation.rd
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@@ -31,5 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
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32 32 
 }
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 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = rowAnnotation(df = df)}
man/component_height-Heatmap-method.rd
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method}
man/component_height-HeatmapList-method.rd
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@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method}
man/component_width-Heatmap-method.rd
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@@ -20,6 +20,7 @@ This function is only for internal use.
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 }
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 \section{Detials}{
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+
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 This function is only for internal use.}
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 \value{
25 26 
 A \code{\link[grid]{unit}} object.
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@@ -30,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method}
man/component_width-HeatmapList-method.rd
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@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method}
man/dist2.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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31 31 
 }
32 32 
 \examples{
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+
33 34 
 mat = matrix(rnorm(40), nr = 4, ncol = 10)
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 rownames(mat) = letters[1:4]
35 36 
 colnames(mat) = letters[1:10]
man/draw-Heatmap-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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32 32 
 }
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 \examples{
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+
34 35 
 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/draw-HeatmapAnnotation-method.rd
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@@ -30,6 +30,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
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 ha = HeatmapAnnotation(df = df)
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 grid.newpage(); draw(ha, 1:6)
man/draw-HeatmapList-method.rd
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@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 mat = matrix(rnorm(80, 2), 8, 10)
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 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
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 rownames(mat) = letters[1:12]
man/draw-SingleAnnotation-method.rd
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@@ -31,6 +31,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
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 grid.newpage(); draw(anno, 1:5)
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 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))
man/draw_annotation-Heatmap-method.rd
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@@ -34,5 +34,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/draw_annotation_legend-HeatmapList-method.rd
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@@ -32,5 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL}
man/draw_dimnames-Heatmap-method.rd
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@@ -35,5 +35,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL}
man/draw_hclust-Heatmap-method.rd
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@@ -42,5 +42,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL}
man/draw_heatmap_body-Heatmap-method.rd
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@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/draw_heatmap_legend-HeatmapList-method.rd
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@@ -32,5 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/draw_heatmap_list-HeatmapList-method.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/draw_title-Heatmap-method.rd
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@@ -33,5 +33,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL}
man/draw_title-HeatmapList-method.rd
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@@ -31,5 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/get_color_mapping_list-HeatmapAnnotation-method.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/grid.dendrogram.rd
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@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 hc = hclust(dist(USArrests[1:5, ]))
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 dend = as.dendrogram(hc)
39 40
man/heatmap_legend_size-HeatmapList-method.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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 # no example for this internal method
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 NULL}
man/make_column_cluster-Heatmap-method.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
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 NULL}
man/make_layout-Heatmap-method.rd
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@@ -33,5 +33,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
35 35 
 \examples{
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+
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 # no example for this internal method
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 NULL}
man/make_layout-HeatmapList-method.rd
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@@ -59,5 +59,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
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 \examples{
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+
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 # no example for this internal method
63 64 
 NULL}
man/make_row_cluster-Heatmap-method.rd
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@@ -32,5 +32,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
34 34 
 \examples{
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+
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 # no example for this internal method
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 NULL}
man/map_to_colors-ColorMapping-method.rd
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@@ -29,6 +29,7 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
30 30 
 }
31 31 
 \examples{
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+
32 33 
 # discrete color mapping for characters
33 34 
 cm = ColorMapping(name = "test",
34 35 
     colors = c("blue", "white", "red"),
man/plot.HeatmapList.rd
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@@ -25,5 +25,6 @@ This function returns no value.
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 }
27 27 
 \examples{
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+
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 # no example
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 NULL}
man/plotDataFrame.rd
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@@ -46,6 +46,7 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
48 48 
 \examples{
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
50 51 
                 large = runif(10)*100,
51 52 
                 t1 = sample(letters[1:3], 10, replace = TRUE),
man/prepare-Heatmap-method.rd
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@@ -37,5 +37,6 @@ Zuguang Gu <z.gu@dkfz.de>
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 }
39 39 
 \examples{
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+
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 # no example for this internal method
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 NULL}
man/print.HeatmapList.rd
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@@ -25,5 +25,6 @@ This function returns no value.
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 }
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 \examples{
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+
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 # no example
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 NULL}
man/rowAnnotation.rd
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@@ -31,5 +31,6 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
32 32 
 }
33 33 
 \examples{
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+
34 35 
 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))
35 36 
 ha = columnAnnotation(df = df)}
man/set_component_height-Heatmap-method.rd
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@@ -30,5 +30,6 @@ Zuguang Gu <z.gu@dkfz.de>
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31 31 
 }
32 32 
 \examples{
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+
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 # no example for this internal method
34 35 
 NULL}
man/show-Heatmap-method.rd
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@@ -28,6 +28,7 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
29 29 
 }
30 30 
 \examples{
31 
+
31 32 
 mat = matrix(rnorm(80, 2), 8, 10)
32 33 
 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
33 34 
 rownames(mat) = letters[1:12]
man/show-HeatmapList-method.rd
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@@ -24,4 +24,5 @@ This function returns no value.
24 24
25 25 
 }
26 26 
 \author{
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+
27 28 
 Zuguang Gu <z.gu@dkfz.de>}